Biomedical Data/Content Acquisition, Curation

Friday, August 1, 2008

Nigam Shah. In the Encyclopedia of Database Systems, (Springer Verlag)
Area Editor: Vipul Kashyap

The largest source of biomedical knowledge is the published literature, where results of experimental studies are reported in natural language. Published literature is hard to query, integrate computationally or to reason over. The task of reading published papers (or other forms of experimental results such as pharmacogenomics datasets) and distilling them down into structured knowledge that can be stored in databases as well as knowledgebases is called curation. The statements comprising the structured knowledge are called annotations. The level of structure in annotation statements can vary from loose declarations of “associations“ between concepts (such as associating a paper with the concept ‘colon cancer’) to statements that declare a precisely defined relationship between concepts with explicit semantics. There is an inherent tradeoff between the level of detail of the structured annotations and the time and effort required to create them. Curation to create highly structured and computable annotations requires PhD level individuals to curate the literature.